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141
The Vienna RNA Secondary Structure Server
- Nucleic Acids Res
, 2003
"... The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus secondary ..."
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Cited by 611 (23 self)
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The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences, and the design of sequences that will fold into a predefined structure.
PF: Secondary structure prediction for aligned RNA sequences.
- J Mol Biol
, 2002
"... Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phy ..."
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Cited by 331 (43 self)
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Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.
Pfold: RNA secondary structure prediction using stochastic context-free grammars
- Nucleic Acids Res
, 2003
"... RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applic ..."
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Cited by 213 (11 self)
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RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses to give improved results. This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained. The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
, 1999
"... Motivation: Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary ..."
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Cited by 180 (16 self)
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Motivation: Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary history into RNA secondary structure prediction. The method reported here is based on stochastic context-free grammars (SCFGs) to give a prior probability distribution of structures.
RSEARCH: Finding homologs of single structured RNA sequences
- BMC Bioinformatics
, 2003
"... Background: Many trans-acting noncoding RNA genes and cis-acting RNA regulatory elements conserve secondary structure rather than primary sequence. Most homology search tools only look at the primary sequence level, however. ..."
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Cited by 170 (3 self)
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Background: Many trans-acting noncoding RNA genes and cis-acting RNA regulatory elements conserve secondary structure rather than primary sequence. Most homology search tools only look at the primary sequence level, however.
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
, 2004
"... Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On ..."
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Cited by 81 (2 self)
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Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On the other hand, comparative methods are more reliable, but are often done in an ad hoc manner and require expert intervention. Maximum weighted matching, an algorithm for pseudoknot prediction with comparative analysis, suffers from low-prediction accuracy in many cases.
CMfinder–a covariance model based RNA motif finding algorithm
- Bioinformatics
, 2006
"... doi:10.1093/bioinformatics/btk008 ..."
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
, 2004
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Predicting a set of minimal free energy RNA secondary structures common to two sequences
- Bioinformatics
, 2005
"... Function derives from structure; therefore there is need of methods for predicting functional RNA structures. Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low energy structu ..."
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Cited by 45 (6 self)
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Function derives from structure; therefore there is need of methods for predicting functional RNA structures. Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20 % of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence. Availability: Dynalign can be downloaded at
Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1
- Mol. Cell Biol
, 2005
"... Updated information and services can be found at: ..."
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